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Merge pull request #350 from broadinstitute/chartl_genotypeconcordance_doc_cleanup 

Add <pre> tags to the Genotype Concordance docs. Tables were not being d...
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chartl 2013-07-29 16:17:26 -07:00
parent 678d038c76 464a5b229d
commit cf46256356
1 changed files with 10 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
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@ -69,12 +69,15 @@ import java.util.*;
* Genotype Concordance writes a GATK report to the specified file (via -o) , consisting of multiple tables of counts * Genotype Concordance writes a GATK report to the specified file (via -o) , consisting of multiple tables of counts
* and proportions. These tables may be optionally moltenized via the -moltenize argument. That is, the standard table * and proportions. These tables may be optionally moltenized via the -moltenize argument. That is, the standard table
* *
* <pre>
* Sample NO_CALL_HOM_REF NO_CALL_HET NO_CALL_HOM_VAR (...) * Sample NO_CALL_HOM_REF NO_CALL_HET NO_CALL_HOM_VAR (...)
* NA12878 0.003 0.001 0.000 (...) * NA12878 0.003 0.001 0.000 (...)
* NA12891 0.005 0.000 0.000 (...) * NA12891 0.005 0.000 0.000 (...)
* </pre>
* *
* would instead be displayed * would instead be displayed
* *
* <pre>
* NA12878 NO_CALL_HOM_REF 0.003 * NA12878 NO_CALL_HOM_REF 0.003
* NA12878 NO_CALL_HET 0.001 * NA12878 NO_CALL_HET 0.001
* NA12878 NO_CALL_HOM_VAR 0.000 * NA12878 NO_CALL_HOM_VAR 0.000
@ -82,6 +85,7 @@ import java.util.*;
* NA12891 NO_CALL_HET 0.000 * NA12891 NO_CALL_HET 0.000
* NA12891 NO_CALL_HOM_VAR 0.000 * NA12891 NO_CALL_HOM_VAR 0.000
* (...) * (...)
* </pre>
* *
* *
* These tables are constructed on a per-sample basis, and include counts of eval vs comp genotype states, and the * These tables are constructed on a per-sample basis, and include counts of eval vs comp genotype states, and the
@ -92,8 +96,10 @@ import java.util.*;
* counts for EVAL_SUBSET_TRUTH and EVAL_SUPERSET_TRUTH will be generated. * counts for EVAL_SUBSET_TRUTH and EVAL_SUPERSET_TRUTH will be generated.
* *
* For example, in the following situation * For example, in the following situation
* <pre>
* eval: ref - A alt - C * eval: ref - A alt - C
* comp: ref - A alt - C,T * comp: ref - A alt - C,T
* </pre>
* then the site is tabulated as EVAL_SUBSET_TRUTH. Were the situation reversed, it would be EVAL_SUPERSET_TRUTH. * then the site is tabulated as EVAL_SUBSET_TRUTH. Were the situation reversed, it would be EVAL_SUPERSET_TRUTH.
* However, in the case where eval has both C and T alternate alleles, both must be observed in the genotypes * However, in the case where eval has both C and T alternate alleles, both must be observed in the genotypes
* (that is, there must be at least one of (0/1,1/1) and at least one of (0/2,1/2,2/2) in the genotype field). If * (that is, there must be at least one of (0/1,1/1) and at least one of (0/2,1/2,2/2) in the genotype field). If
@ -106,11 +112,15 @@ import java.util.*;
* (if no record exists in the comp VCF). * (if no record exists in the comp VCF).
* *
* That is, in the situation * That is, in the situation
* <pre>
* eval: ref - A alt - C genotypes - 0/0 0/0 0/0 ... 0/0 * eval: ref - A alt - C genotypes - 0/0 0/0 0/0 ... 0/0
* comp: ref - A alt - C ... 0/0 0/0 ... * comp: ref - A alt - C ... 0/0 0/0 ...
* </pre>
* is equivalent to * is equivalent to
* <pre>
* eval: ref - A alt - . genotypes - 0/0 0/0 0/0 ... 0/0 * eval: ref - A alt - . genotypes - 0/0 0/0 0/0 ... 0/0
* comp: ref - A alt - C ... 0/0 0/0 ... * comp: ref - A alt - C ... 0/0 0/0 ...
* </pre>
* *
* When a record is present in the comp VCF the *genotypes* for the monomorphic site will still be used to evaluate * When a record is present in the comp VCF the *genotypes* for the monomorphic site will still be used to evaluate
* per-sample genotype concordance counts. * per-sample genotype concordance counts.